I've seen this happen pretty often due to supply issues. The easy way to handle this is keep the Pip-Boy, case, poster, etc, sell the PC version, and then just buy the non-limited PS4 regular Fallout 4 game.
I only WISH I had this problem... because then I would do exactly what MVJ suggested. Hell, I had already planned on buying two copies. A Pipboy Edition and a regular version on Steam. The plan was to use the Steam version for pre-loading and launch-second play, and then sell the code that came with my Pipboy Edition to someone slightly below retail price.
Here's hoping they announce more Pipboy Editions and I can actually act on that plan. :/
http://store.gamesas.com/collectibles/fallout-4-pip-boy-edition.html.
Just cancel the order on the PC one and pre-order the PS4 one, shouldn't be a problem. Or you could do it in the oposite order so you're guaranteed a pip-boy edition either way.